Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012682.1 Corchorus capsularis cultivar CVL-1 contig12703, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10605
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Found at i:1345 original size:9 final size:9
Alignment explanation
Indices: 1331--1365 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1321 TTCTGGTTGA
1331 AATTTTTTT
1 AATTTTTTT
1340 AATTTTTTT
1 AATTTTTTT
*
1349 TATTTTTTT
1 AATTTTTTT
1358 ATATTTTT
1 A-ATTTTT
1366 CGATATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
AATTTTTTT
Found at i:2725 original size:21 final size:21
Alignment explanation
Indices: 2680--2733 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2670 TTTACTGAAT
*
2680 TACTGATTACTATTACTATTT
1 TACTGATTACTATTACTATTG
2701 TACTGATTATTCT-TTACT-TTG
1 TACTGATTA--CTATTACTATTG
2722 TACTGATTACTA
1 TACTGATTACTA
2734 GTCACCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.07
21 20 0.69
22 5 0.17
23 2 0.07
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (21 bp):
TACTGATTACTATTACTATTG
Found at i:2839 original size:34 final size:34
Alignment explanation
Indices: 2764--2893 Score: 99
Period size: 34 Copynumber: 3.8 Consensus size: 34
2754 TGAATGCCAT
* * * *
2764 TTCTT-TTTACTGATTAATATTTTACCCTTTACGA
1 TTCTTCTTTACTGATTACT-CTTTACTCTTTACCA
* *
2798 TTTTTCTTTACTGATTACTCTTTACTCTTCACCA
1 TTCTTCTTTACTGATTACTCTTTACTCTTTACCA
* * *
2832 TTCTTCTTCT-CTGACTT-CTCCTCACTTTTTACCA
1 TTCTTCTT-TACTGA-TTACTCTTTACTCTTTACCA
2866 TT-TTCCTTTGA-TGATTACTCTTTACTCT
1 TTCTT-CTTT-ACTGATTACTCTTTACTCT
2894 ACTCTTTACT
Statistics
Matches: 75, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
33 5 0.07
34 55 0.73
35 15 0.20
ACGTcount: A:0.17, C:0.25, G:0.05, T:0.53
Consensus pattern (34 bp):
TTCTTCTTTACTGATTACTCTTTACTCTTTACCA
Found at i:2892 original size:7 final size:7
Alignment explanation
Indices: 2880--3475 Score: 137
Period size: 7 Copynumber: 88.4 Consensus size: 7
2870 CCTTTGATGA
2880 TTACTCT
1 TTACTCT
2887 TTACTC-
1 TTACTCT
2893 -TACTCT
1 TTACTCT
2899 TTACTCT
1 TTACTCT
2906 TTAC-CAT
1 TTACTC-T
*
2913 TT-TTC-
1 TTACTCT
**
2918 TTACTGA
1 TTACTCT
2925 TTACTCT
1 TTACTCT
2932 TT-C-CT
1 TTACTCT
* *
2937 CTACTGT
1 TTACTCT
2944 TTACTCT
1 TTACTCT
2951 TTAC-CT
1 TTACTCT
*
2957 TT-TTCT
1 TTACTCT
**
2963 TTACTGA
1 TTACTCT
2970 TTACTCT
1 TTACTCT
2977 TT-C-CT
1 TTACTCT
2982 TTACTCT
1 TTACTCT
2989 TTACTCT
1 TTACTCT
*
2996 TTACCCT
1 TTACTCT
*
3003 TT-TTCT
1 TTACTCT
**
3009 TTACTGA
1 TTACTCT
3016 TTACTCTT
1 TTACTC-T
*
3024 TTACTTT
1 TTACTCT
3031 TTAC-CAT
1 TTACTC-T
3038 TT--TACT
1 TTACT-CT
* **
3044 TTGCTGA
1 TTACTCT
3051 TTACTCT
1 TTACTCT
* *
3058 TTATTTT
1 TTACTCT
3065 TTAC-CAT
1 TTACTC-T
3072 TT--TACT
1 TTACT-CT
* **
3078 TTGCTGA
1 TTACTCT
3085 TTACTCT
1 TTACTCT
3092 TTACT-T
1 TTACTCT
*
3098 CTACTCT
1 TTACTCT
3105 TTACTCT
1 TTACTCT
3112 TTAC-CAT
1 TTACTC-T
*
3119 TT-TTCT
1 TTACTCT
**
3125 TTACTGA
1 TTACTCT
3132 TTACTCT
1 TTACTCT
3139 TT-C-CT
1 TTACTCT
3144 TTACTCT
1 TTACTCT
3151 TTACTCT
1 TTACTCT
*
3158 TTACCCT
1 TTACTCT
*
3165 TT-TTCT
1 TTACTCT
**
3171 TTACTGA
1 TTACTCT
3178 TTACTCTT
1 TTACTC-T
*
3186 TTACTTT
1 TTACTCT
3193 TTAC-CAT
1 TTACTC-T
3200 TT--TACT
1 TTACT-CT
* **
3206 TTGCTGA
1 TTACTCT
3213 TTACTCT
1 TTACTCT
*
3220 TTACTTT
1 TTACTCT
3227 TTAC-CAT
1 TTACTC-T
3234 TT--TACT
1 TTACT-CT
* **
3240 TTGCTGA
1 TTACTCT
3247 TTACTCT
1 TTACTCT
*
3254 TTACTTT
1 TTACTCT
3261 TTAC-CAT
1 TTACTC-T
3268 TT--TACT
1 TTACT-CT
* **
3274 TTGCTGA
1 TTACTCT
3281 TTACTCT
1 TTACTCT
3288 TTA--CT
1 TTACTCT
3293 TTACTCT
1 TTACTCT
*
3300 TTACTTT
1 TTACTCT
*
3307 TTACCCT
1 TTACTCT
*
3314 TT-TTCT
1 TTACTCT
**
3320 TTACTGA
1 TTACTCT
3327 TTACTCCT
1 TTACT-CT
*
3335 TTACTTT
1 TTACTCT
3342 TTAC-CAT
1 TTACTC-T
3349 TT--TACT
1 TTACT-CT
* **
3355 TTGCTGA
1 TTACTCT
3362 TTACTCT
1 TTACTCT
*
3369 TTACTTT
1 TTACTCT
3376 TTAC-CAT
1 TTACTC-T
3383 TT--TACT
1 TTACT-CT
* **
3389 TTGCTGA
1 TTACTCT
3396 TTACTCT
1 TTACTCT
3403 TTA--CT
1 TTACTCT
3408 TTACTCT
1 TTACTCT
*
3415 TTACTTT
1 TTACTCT
3422 TTACTCT
1 TTACTCT
*
3429 TTACCATTT
1 TTA-C-TCT
**
3438 TTTTTCT
1 TTACTCT
**
3445 TTACTGA
1 TTACTCT
* *
3452 TTGCTCC
1 TTACTCT
3459 TTACTCT
1 TTACTCT
3466 TTACTCT
1 TTACTCT
3473 TTA
1 TTA
3476 TCATTTCTTA
Statistics
Matches: 409, Mismatches: 115, Indels: 130
0.63 0.18 0.20
Matches are distributed among these distances:
5 28 0.07
6 58 0.14
7 296 0.72
8 23 0.06
9 4 0.01
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.57
Consensus pattern (7 bp):
TTACTCT
Found at i:2898 original size:12 final size:12
Alignment explanation
Indices: 2881--2905 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2871 CTTTGATGAT
2881 TACTCTTTACTC
1 TACTCTTTACTC
2893 TACTCTTTACTC
1 TACTCTTTACTC
2905 T
1 T
2906 TTACCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTCTTTACTC
Found at i:2909 original size:26 final size:26
Alignment explanation
Indices: 2880--3166 Score: 72
Period size: 26 Copynumber: 11.3 Consensus size: 26
2870 CCTTTGATGA
2880 TTACTCTTTACTCTACTCTTTACTCT
1 TTACTCTTTACTCTACTCTTTACTCT
* **
2906 TTAC-CATT--T-T--TC-TTACTGA
1 TTACTCTTTACTCTACTCTTTACTCT
* *
2925 TTACTCTTTCCTCTACTGTTTACTCT
1 TTACTCTTTACTCTACTCTTTACTCT
* * **
2951 TTAC-CTTTTTCTTTACTGATTACTCT
1 TTACTC-TTTACTCTACTCTTTACTCT
*
2977 TT-C-CTTTACTCTTTACTCTTTACCCT
1 TTACTCTTTACTC--TACTCTTTACTCT
* * *
3003 TT-TTCTTTACTGATTACTCTTTTACTTT
1 TTACTCTTTACT--CTACTC-TTTACTCT
* * **
3031 TTAC-CATTTTACTTTGCTGATTACTCT
1 TTACTC--TTTACTCTACTCTTTACTCT
* * ** * **
3058 TTATTTTTTAC-CATTTTACTTTGCTGA
1 TTACTCTTTACTC-TACT-CTTTACTCT
3085 TTACTCTTTACTTCTACTCTTTACTCT
1 TTACTCTTTAC-TCTACTCTTTACTCT
* **
3112 TTAC-CATT--T-T--TCTTTACTGA
1 TTACTCTTTACTCTACTCTTTACTCT
* *
3132 TTACTCTTTCCTTTACTCTTTACTCT
1 TTACTCTTTACTCTACTCTTTACTCT
*
3158 TTACCCTTT
1 TTACTCTTT
3167 TTCTTTACTG
Statistics
Matches: 185, Mismatches: 48, Indels: 56
0.64 0.17 0.19
Matches are distributed among these distances:
19 9 0.05
20 17 0.09
21 3 0.02
22 3 0.02
23 4 0.02
24 6 0.03
25 7 0.04
26 70 0.38
27 44 0.24
28 15 0.08
29 1 0.01
30 6 0.03
ACGTcount: A:0.15, C:0.25, G:0.03, T:0.56
Consensus pattern (26 bp):
TTACTCTTTACTCTACTCTTTACTCT
Found at i:2932 original size:45 final size:46
Alignment explanation
Indices: 2859--3186 Score: 348
Period size: 46 Copynumber: 7.7 Consensus size: 46
2849 CTCCTCACTT
* *
2859 TTTACCATTTTCCTTTGA-TGATTACTCTTTACTCTACTCTTTACTC
1 TTTACCATTTTTCTTT-ACTGATTACTCTTTCCTCTACTCTTTACTC
*
2905 TTTACCATTTTTC-TTACTGATTACTCTTTCCTCTACTGTTTACTC
1 TTTACCATTTTTCTTTACTGATTACTCTTTCCTCTACTCTTTACTC
*
2950 TTTACC-TTTTTCTTTACTGATTACTCTTTCCTTTACTCTTTACTC
1 TTTACCATTTTTCTTTACTGATTACTCTTTCCTCTACTCTTTACTC
*
2995 TTTACCCTTTTTCTTTACTGATTACTC-TT--T-TA--C--T--T-
1 TTTACCATTTTTCTTTACTGATTACTCTTTCCTCTACTCTTTACTC
* *
3030 TTTACCATTTTACTTTGCTGATTACTC--T--T-TA----TT--T-
1 TTTACCATTTTTCTTTACTGATTACTCTTTCCTCTACTCTTTACTC
* * *
3064 TTTACCATTTTACTTTGCTGATTACTCTTTACTTCTACTCTTTACTC
1 TTTACCATTTTTCTTTACTGATTACTCTTT-CCTCTACTCTTTACTC
*
3111 TTTACCATTTTTCTTTACTGATTACTCTTTCCTTTACTCTTTACTC
1 TTTACCATTTTTCTTTACTGATTACTCTTTCCTCTACTCTTTACTC
*
3157 TTTACCCTTTTTCTTTACTGATTACTCTTT
1 TTTACCATTTTTCTTTACTGATTACTCTTT
3187 TACTTTTTAC
Statistics
Matches: 252, Mismatches: 13, Indels: 34
0.84 0.04 0.11
Matches are distributed among these distances:
34 33 0.13
35 24 0.10
36 2 0.01
38 1 0.00
39 1 0.00
40 3 0.01
42 2 0.01
43 1 0.00
44 9 0.04
45 72 0.29
46 76 0.30
47 28 0.11
ACGTcount: A:0.16, C:0.25, G:0.04, T:0.56
Consensus pattern (46 bp):
TTTACCATTTTTCTTTACTGATTACTCTTTCCTCTACTCTTTACTC
Found at i:2965 original size:19 final size:19
Alignment explanation
Indices: 2943--2997 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
2933 TCCTCTACTG
*
2943 TTTACTCTTTACCTTTTTC
1 TTTACTCTTTACCTTTTCC
**
2962 TTTACTGATTA-CTCTTTCC
1 TTTACTCTTTACCT-TTTCC
2981 TTTACTCTTTACTCTTT
1 TTTACTCTTTAC-CTTT
2998 ACCCTTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.07
19 22 0.79
20 2 0.07
21 2 0.07
ACGTcount: A:0.13, C:0.25, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTACTCTTTACCTTTTCC
Found at i:3019 original size:20 final size:20
Alignment explanation
Indices: 2954--3030 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 20
2944 TTACTCTTTA
2954 CCTTTTTCTTTACTGATTACTC
1 CCTTTTTCTTTACTGATTA--C
* **
2976 TTTCCTTTACTCTTTACTCTTTAC
1 ---CCTTT-TTCTTTACTGATTAC
3000 CCTTTTTCTTTACTGATTAC
1 CCTTTTTCTTTACTGATTAC
* *
3020 TCTTTTACTTT
1 CCTTTTTCTTT
3031 TTACCATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
20 21 0.49
21 5 0.12
24 1 0.02
25 5 0.12
26 11 0.26
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.58
Consensus pattern (20 bp):
CCTTTTTCTTTACTGATTAC
Found at i:3032 original size:27 final size:26
Alignment explanation
Indices: 2970--3343 Score: 76
Period size: 27 Copynumber: 13.3 Consensus size: 26
2960 TCTTTACTGA
* *
2970 TTACTCTTTCCTTTACTCTTTACTCT
1 TTACTTTTTCCTTTACTCATTACTCT
*
2996 TTACCCTTTTT-CTTTACTGATTACTCTT
1 TTA--CTTTTTCCTTTACTCATTACTC-T
3024 TTACTTTTTACCATTTTACTTTGCTGATTACTCT
1 TTACTTTTT-CC--TTTAC--T-C--ATTACTCT
* * **
3058 TTATTTTTTACCATTTTACT--TTGCTGA
1 TTACTTTTT-CC--TTTACTCATTACTCT
* * *
3085 TTACTCTTTACTTCTACTCTTTACTCT
1 TTACTTTTTCCTT-TACTCATTACTCT
*
3112 TTACCATTTTT-CTTTACTGATTA--C-
1 TTA-C-TTTTTCCTTTACTCATTACTCT
*
3136 -T-C--TTTCCTTTACTCTTTACTCT
1 TTACTTTTTCCTTTACTCATTACTCT
*
3158 TTACCCTTTTT-CTTTACTGATTACTCTT
1 TTA--CTTTTTCCTTTACTCATTACTC-T
3186 TTACTTTTTACCATTTTACTTTGCTGATTACTCT
1 TTACTTTTT-CC--TTTAC--T-C--ATTACTCT
3220 TTACTTTTTACCATTTTACTTTGCTGATTACTCT
1 TTACTTTTT-CC--TTTAC--T-C--ATTACTCT
* **
3254 TTACTTTTTACCATTTTACT--TTGCTGA
1 TTACTTTTT-CC--TTTACTCATTACTCT
* * * *
3281 TTACTCTTTACTTTACTCTTTACTTT
1 TTACTTTTTCCTTTACTCATTACTCT
*
3307 TTACCCTTTTT-CTTTACTGATTACTCCT
1 TTA--CTTTTTCCTTTACTCATTACT-CT
3335 TTACTTTTT
1 TTACTTTTT
3344 ACCATTTTAC
Statistics
Matches: 272, Mismatches: 34, Indels: 84
0.70 0.09 0.22
Matches are distributed among these distances:
18 3 0.01
19 10 0.04
21 2 0.01
23 2 0.01
24 8 0.03
25 5 0.02
26 31 0.11
27 75 0.28
28 31 0.11
29 4 0.01
30 10 0.04
32 4 0.01
34 73 0.27
35 14 0.05
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.57
Consensus pattern (26 bp):
TTACTTTTTCCTTTACTCATTACTCT
Found at i:3059 original size:81 final size:81
Alignment explanation
Indices: 2943--3226 Score: 339
Period size: 81 Copynumber: 3.5 Consensus size: 81
2933 TCCTCTACTG
*
2943 TTTACTCTTTACC-TTTTTCTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTT
1 TTTACTCTTTACCATTTTACTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTT
3007 CTTTACTGATTACTCT
66 CTTTACTGATTACTCT
* * ** * **
3023 TTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTATTTTTTAC-CATTT--TACTTTGCTGA
1 TTTACTCTTTACCATTTTACTTTACTGATTACTC-TT-TCCTTTACTC-TTTACT-CTTTAC-CC
**
3085 TTACTCTTTACT--TCTACTC-
61 TTTTTCTTTACTGAT-TACTCT
*
3104 TTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTT
1 TTTACTCTTTACCATTTTACTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTT
3169 CTTTACTGATTACTCT
66 CTTTACTGATTACTCT
* * *
3185 TTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTT
1 TTTACTCTTTACCATTTTACTTTACTGATTACTCTTTCCTTT
3227 TTACCATTTT
Statistics
Matches: 167, Mismatches: 24, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
79 19 0.11
80 25 0.15
81 91 0.54
82 13 0.08
83 19 0.11
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (81 bp):
TTTACTCTTTACCATTTTACTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTT
CTTTACTGATTACTCT
Found at i:3071 original size:34 final size:34
Alignment explanation
Indices: 2982--3294 Score: 348
Period size: 34 Copynumber: 9.4 Consensus size: 34
2972 ACTCTTTCCT
* * * *
2982 TTACTCTTTACTCTTTACCCTTTTTCTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
3016 TTACTCTTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTC-TTTACTTTTTACCATTTTACTTTGCTGA
*
3051 TTACTCTTTATTTTTTACCATTTTACTTTGCTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
*
3085 TTACTCTTTAC-TTCTA-C-TCTTTAC--T-CT--
1 TTACTCTTTACTTTTTACCAT-TTTACTTTGCTGA
* * *
3112 TTAC-CATTT--TTCTTTACTGATTACT-CTTTCCT--
1 TTACTC-TTTACTT-TTTAC-CATT-TTACTTTGCTGA
* * * *
3144 TTACTCTTTACTCTTTACCCTTTTTCTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
3178 TTACTCTTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTC-TTTACTTTTTACCATTTTACTTTGCTGA
3213 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
3247 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
3281 TTACTCTTTACTTT
1 TTACTCTTTACTTT
3295 ACTCTTTACT
Statistics
Matches: 241, Mismatches: 19, Indels: 38
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.01
27 10 0.04
29 4 0.02
30 3 0.01
31 3 0.01
32 23 0.10
33 10 0.04
34 126 0.52
35 60 0.25
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.57
Consensus pattern (34 bp):
TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
Found at i:3088 original size:20 final size:20
Alignment explanation
Indices: 3031--3088 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
3021 CTTTTACTTT
3031 TTACCATTTTACTTTGCTGA
1 TTACCATTTTACTTTGCTGA
3051 TTA-C-TCTTTA-TTT--T--
1 TTACCAT-TTTACTTTGCTGA
3065 TTACCATTTTACTTTGCTGA
1 TTACCATTTTACTTTGCTGA
3085 TTAC
1 TTAC
3089 TCTTTACTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
14 3 0.10
15 5 0.17
16 5 0.17
18 5 0.17
19 5 0.17
20 7 0.23
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (20 bp):
TTACCATTTTACTTTGCTGA
Found at i:3113 original size:149 final size:148
Alignment explanation
Indices: 2960--3426 Score: 697
Period size: 149 Copynumber: 3.1 Consensus size: 148
2950 TTTACCTTTT
2960 TCTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTT
1 TCTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTT
*
3025 TACTTTTTACCATTTTACTTTGCTGATTACTCTTTATTTTTTACCATTTTACTTTGCTGATTACT
66 TACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGCTGATTA--
3090 CTTTACTTCTACTCTTTACTCTTTACC
129 C--T-CTT-TA--CTTTACTCTTTA-C
3117 ATTTTTCTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTTCTTTACTGATTAC
1 -----TCTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTTCTTTACTGATTAC
3182 TCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGCTGA
61 TCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGCTGA
3247 TTACTCTTTACTTTTTAC-CATTT--
126 TTACTCTTTAC--TTTACTC-TTTAC
* * * *
3270 TACTTTGCTGATTACTCTTTACTTTACTCTTTACTTTTTACCCTTTTTCTTTACTGATTACTCCT
1 T-CTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTT
3335 TTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGCTGATTAC
65 TTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGCTGATTAC
3400 TCTTTACTTTACTCTTTAC
130 TCTTTACTTTACTCTTTAC
*
3419 TTTTTACT
1 TCTTTACT
3427 CTTTACCATT
Statistics
Matches: 291, Mismatches: 7, Indels: 28
0.89 0.02 0.09
Matches are distributed among these distances:
147 8 0.03
148 7 0.02
149 132 0.45
154 1 0.00
155 1 0.00
156 10 0.03
157 3 0.01
158 1 0.00
160 1 0.00
162 127 0.44
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.57
Consensus pattern (148 bp):
TCTTTACTGATTACTCTTTCCTTTACTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTT
TACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGCTGATTACT
CTTTACTTTACTCTTTAC
Found at i:3125 original size:20 final size:20
Alignment explanation
Indices: 3102--3175 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
3092 TTACTTCTAC
3102 TCTTTACTCTTTACCATTTT
1 TCTTTACTCTTTACCATTTT
** *
3122 TCTTTACTGATTACTCTTTCCTTT
1 TCTTTACTCTTTAC-C-AT--TTT
*
3146 ACTCTTTACTCTTTACCCTTTT
1 --TCTTTACTCTTTACCATTTT
3168 TCTTTACT
1 TCTTTACT
3176 GATTACTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 20 0.48
21 1 0.02
22 4 0.10
24 4 0.10
25 1 0.02
26 12 0.29
ACGTcount: A:0.14, C:0.27, G:0.01, T:0.58
Consensus pattern (20 bp):
TCTTTACTCTTTACCATTTT
Found at i:3147 original size:19 final size:19
Alignment explanation
Indices: 3123--3159 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3113 TACCATTTTT
*
3123 CTTTACTGATTACTCTTTC
1 CTTTACTCATTACTCTTTC
*
3142 CTTTACTCTTTACTCTTT
1 CTTTACTCATTACTCTTT
3160 ACCCTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.03, T:0.57
Consensus pattern (19 bp):
CTTTACTCATTACTCTTTC
Found at i:3181 original size:20 final size:20
Alignment explanation
Indices: 3102--3192 Score: 56
Period size: 20 Copynumber: 4.2 Consensus size: 20
3092 TTACTTCTAC
* *
3102 TCTTTACTCTTTACCATTTT
1 TCTTTACTCATTACCCTTTT
* *
3122 TCTTTACTGATTACTCTTTCCTTTAC
1 TCTTTACTCATTA--C---CCTTT-T
*
3148 TCTTTACTCTTTACCCTTTT
1 TCTTTACTCATTACCCTTTT
* *
3168 TCTTTACTGATTACTCTTTT
1 TCTTTACTCATTACCCTTTT
*
3188 ACTTT
1 TCTTT
3193 TTACCATTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
20 32 0.59
21 5 0.09
22 1 0.02
24 1 0.02
25 4 0.07
26 11 0.20
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.58
Consensus pattern (20 bp):
TCTTTACTCATTACCCTTTT
Found at i:3248 original size:115 final size:112
Alignment explanation
Indices: 2982--3425 Score: 402
Period size: 115 Copynumber: 3.9 Consensus size: 112
2972 ACTCTTTCCT
* * * * * *
2982 TTACTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTG
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGATTACTC-TTT-C-CTTTACCATTTTACTTTA
* * * * *
3047 CTGATTACTCTTTATTTTTTAC-CATTTTAC--TTTGCTGATTACT-CTTTACT--
63 CTCATTACTCTTTA--CTTTACTC--TTTACTTTTTAC-CATT-TTACTTTACTGA
* * *
3097 TCTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTCCTTTA-C-TCTTTACTCTTT
1 T-TACTCTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTCCTTTACCAT-TTTA--CTTT
* ** *
3160 AC-CCTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGA
62 ACTCATTACTCTTTACT--TTACTC-TTTACTTTTTACCATTTTACTTTACTGA
* *
3213 TTACTCTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGC
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTT-C-CTTTACCATTTTACTTTAC
* * *
3278 TGATTACTCTTTACTTTACTCTTTACTTTTTACCCTTTTTCTTTACTGA
64 TCATTACTCTTTACTTTACTCTTTACTTTTTACCATTTTACTTTACTGA
* *
3327 TTACTCCTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTG
1 TTACT-CTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTT-C-CTTTACCATTTTACTTTA
*
3392 CTGATTACTCTTTACTTTACTCTTTACTTTTTAC
63 CTCATTACTCTTTACTTTACTCTTTACTTTTTAC
3426 TCTTTACCAT
Statistics
Matches: 287, Mismatches: 24, Indels: 36
0.83 0.07 0.10
Matches are distributed among these distances:
111 2 0.01
112 5 0.02
113 23 0.08
114 46 0.16
115 146 0.51
116 45 0.16
117 14 0.05
118 5 0.02
119 1 0.00
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.57
Consensus pattern (112 bp):
TTACTCTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTCCTTTACCATTTTACTTTACTC
ATTACTCTTTACTTTACTCTTTACTTTTTACCATTTTACTTTACTGA
Found at i:3250 original size:20 final size:20
Alignment explanation
Indices: 3193--3284 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 20
3183 CTTTTACTTT
3193 TTACCATTTTACTTTGCTGA
1 TTACCATTTTACTTTGCTGA
3213 TTA-C-TCTTTAC-TT--T--
1 TTACCAT-TTTACTTTGCTGA
3227 TTACCATTTTACTTTGCTGA
1 TTACCATTTTACTTTGCTGA
3247 TTA-C-TCTTTAC-TT--T--
1 TTACCAT-TTTACTTTGCTGA
3261 TTACCATTTTACTTTGCTGA
1 TTACCATTTTACTTTGCTGA
3281 TTAC
1 TTAC
3285 TCTTTACTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 32
0.64 0.00 0.36
Matches are distributed among these distances:
14 6 0.11
15 12 0.21
16 8 0.14
18 8 0.14
19 12 0.21
20 10 0.18
ACGTcount: A:0.18, C:0.21, G:0.07, T:0.54
Consensus pattern (20 bp):
TTACCATTTTACTTTGCTGA
Found at i:3296 original size:12 final size:12
Alignment explanation
Indices: 3281--3306 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3271 ACTTTGCTGA
3281 TTACTCTTTACT
1 TTACTCTTTACT
3293 TTACTCTTTACT
1 TTACTCTTTACT
3305 TT
1 TT
3307 TTACCCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTACTCTTTACT
Found at i:3330 original size:20 final size:21
Alignment explanation
Indices: 3297--3336 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3287 TTTACTTTAC
**
3297 TCTTTACTTTTTAC-CCTTTT
1 TCTTTACTGATTACTCCTTTT
3317 TCTTTACTGATTACTCCTTT
1 TCTTTACTGATTACTCCTTT
3337 ACTTTTTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.12, C:0.25, G:0.03, T:0.60
Consensus pattern (21 bp):
TCTTTACTGATTACTCCTTTT
Found at i:3365 original size:20 final size:20
Alignment explanation
Indices: 3342--3399 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
3332 CCTTTACTTT
3342 TTACCATTTTACTTTGCTGA
1 TTACCATTTTACTTTGCTGA
3362 TTA-C-TCTTTAC-TT--T--
1 TTACCAT-TTTACTTTGCTGA
3376 TTACCATTTTACTTTGCTGA
1 TTACCATTTTACTTTGCTGA
3396 TTAC
1 TTAC
3400 TCTTTACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
14 3 0.10
15 6 0.20
16 4 0.13
18 4 0.13
19 6 0.20
20 7 0.23
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (20 bp):
TTACCATTTTACTTTGCTGA
Found at i:3365 original size:81 final size:80
Alignment explanation
Indices: 3213--3375 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 80
3203 ACTTTGCTGA
*
3213 TTACTCTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTTTACCATTTTACTTTGC
1 TTACTCTTTACTTTTTACCATTTTACTTTACTGATTACTCTTTACTTTTTACCATTTTACTTTGC
3278 TGATTACTCTTTACT
66 TGATTACTCTTTACT
* *
3293 TTACTCTTTACTTTTTACCCTTTTTCTTTACTGATTACTCCTTTACTTTTTACCATTTTACTTTG
1 TTACTCTTTACTTTTTACCATTTTACTTTACTGATTACT-CTTTACTTTTTACCATTTTACTTTG
3358 CTGATTACTCTTTACT
65 CTGATTACTCTTTACT
3374 TT
1 TT
3376 TTACCATTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 36 0.46
81 43 0.54
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.57
Consensus pattern (80 bp):
TTACTCTTTACTTTTTACCATTTTACTTTACTGATTACTCTTTACTTTTTACCATTTTACTTTGC
TGATTACTCTTTACT
Found at i:3376 original size:34 final size:34
Alignment explanation
Indices: 3293--3409 Score: 198
Period size: 34 Copynumber: 3.4 Consensus size: 34
3283 ACTCTTTACT
* * *
3293 TTACTCTTTACTTTTTACCCTTTTTCTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
3327 TTACTCCTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACT-CTTTACTTTTTACCATTTTACTTTGCTGA
3362 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
3396 TTACTCTTTACTTT
1 TTACTCTTTACTTT
3410 ACTCTTTACT
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
34 48 0.61
35 31 0.39
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.57
Consensus pattern (34 bp):
TTACTCTTTACTTTTTACCATTTTACTTTGCTGA
Found at i:3520 original size:21 final size:22
Alignment explanation
Indices: 3490--3774 Score: 215
Period size: 21 Copynumber: 13.4 Consensus size: 22
3480 TTCTTACTAA
3490 TTACTCTTT-CTGATTACTCTT
1 TTACTCTTTACTGATTACTCTT
* *
3511 TTACTCTTTCACTAATTGC-CTT
1 TTACTCTTT-ACTGATTACTCTT
* *
3533 TTGCTTTTTACTGATTAC-CTT
1 TTACTCTTTACTGATTACTCTT
3554 TTACT-TCTTACTGATTAGCT-TT
1 TTACTCT-TTACTGATTA-CTCTT
3576 TTACTCTTTACTGATTAGCT-TT
1 TTACTCTTTACTGATTA-CTCTT
3598 TTACTC-TTACTGATTAGCT-TT
1 TTACTCTTTACTGATTA-CTCTT
*
3619 TTACTCTTTATTGATTAGCT-TT
1 TTACTCTTTACTGATTA-CTCTT
*
3641 TTACTC-TTACTAATTAC-CTT
1 TTACTCTTTACTGATTACTCTT
* * * *
3661 TTACTTTTTACTTACTACTGTT
1 TTACTCTTTACTGATTACTCTT
3683 TTACTC-TTACTGATTAC-CTT
1 TTACTCTTTACTGATTACTCTT
* * * *
3703 TTACTTTTTATTGACTACTATT
1 TTACTCTTTACTGATTACTCTT
*
3725 TTACTC-TTACAGATT-C-CTAT
1 TTACTCTTTACTGATTACTCT-T
* * ** *
3745 TTACTTTTTGCCAATTACTATT
1 TTACTCTTTACTGATTACTCTT
3767 TTACTCTT
1 TTACTCTT
3775 GAACGACTTA
Statistics
Matches: 215, Mismatches: 33, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.00
20 23 0.11
21 101 0.47
22 82 0.38
23 8 0.04
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.54
Consensus pattern (22 bp):
TTACTCTTTACTGATTACTCTT
Found at i:3586 original size:43 final size:43
Alignment explanation
Indices: 3490--3774 Score: 264
Period size: 42 Copynumber: 6.7 Consensus size: 43
3480 TTCTTACTAA
*
3490 TTACTCTTT-CTGATTACTCTTTTACTCTTTCACTAATT-GCCTT
1 TTACTCTTTACTGATTACTCTTTTACTC-TT-ACTGATTAGCCTT
* * *
3533 TTGCTTTTTACTGATTAC-CTTTTACTTCTTACTGATTAGCTTT
1 TTACTCTTTACTGATTACTCTTTTAC-TCTTACTGATTAGCCTT
*
3576 TTACTCTTTACTGATTAGCT-TTTTACTCTTACTGATTAGCTTT
1 TTACTCTTTACTGATTA-CTCTTTTACTCTTACTGATTAGCCTT
* *
3619 TTACTCTTTATTGATTAGCT-TTTTACTCTTACTAATTA-CCTT
1 TTACTCTTTACTGATTA-CTCTTTTACTCTTACTGATTAGCCTT
* * * *
3661 TTACTTTTTACTTACTACTGTTTTACTCTTACTGATTA-CCTT
1 TTACTCTTTACTGATTACTCTTTTACTCTTACTGATTAGCCTT
* * * * *
3703 TTACTTTTTATTGACTACTATTTTACTCTTACAGATT--CCTAT
1 TTACTCTTTACTGATTACTCTTTTACTCTTACTGATTAGCCT-T
* * ** *
3745 TTACTTTTTGCCAATTACTATTTTACTCTT
1 TTACTCTTTACTGATTACTCTTTTACTCTT
3775 GAACGACTTA
Statistics
Matches: 212, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
41 5 0.02
42 102 0.48
43 88 0.42
44 17 0.08
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.54
Consensus pattern (43 bp):
TTACTCTTTACTGATTACTCTTTTACTCTTACTGATTAGCCTT
Found at i:3671 original size:14 final size:13
Alignment explanation
Indices: 3530--3712 Score: 62
Period size: 14 Copynumber: 13.0 Consensus size: 13
3520 CACTAATTGC
*
3530 CTTTTGCTTTTTA
1 CTTTTACTTTTTA
* *
3543 CTGATTACCTTTTA
1 CT-TTTACTTTTTA
**
3557 CTTCTTACTGATTA
1 CTT-TTACTTTTTA
*
3571 GCTTTTTACTCTTTA
1 -C-TTTTACTTTTTA
*
3586 CTGATTAGCTTTTTA
1 CT-TTTA-CTTTTTA
* **
3601 CTCTTACTGATTA
1 CTTTTACTTTTTA
*
3614 GCTTTTTACTCTTTA
1 -C-TTTTACTTTTTA
3629 -TTGATTAGCTTTTTA
1 CTT--TTA-CTTTTTA
* **
3644 CTCTTACTAATTA
1 CTTTTACTTTTTA
3657 CCTTTTACTTTTTA
1 -CTTTTACTTTTTA
*
3671 CTTACTACTGTTTTA
1 CTT-TTACT-TTTTA
* **
3686 CTCTTACTGATTA
1 CTTTTACTTTTTA
3699 CCTTTTACTTTTTA
1 -CTTTTACTTTTTA
3713 TTGACTACTA
Statistics
Matches: 122, Mismatches: 32, Indels: 31
0.66 0.17 0.17
Matches are distributed among these distances:
12 2 0.02
13 19 0.16
14 59 0.48
15 39 0.32
16 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.56
Consensus pattern (13 bp):
CTTTTACTTTTTA
Found at i:7375 original size:21 final size:21
Alignment explanation
Indices: 7351--7394 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
7341 AATGCCCTAG
7351 TACCACTTAAATCCTATTTTA
1 TACCACTTAAATCCTATTTTA
*
7372 TACCACTTAACTCCTATTTTA
1 TACCACTTAAATCCTATTTTA
7393 TA
1 TA
7395 GGGCCTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (21 bp):
TACCACTTAAATCCTATTTTA
Found at i:8775 original size:33 final size:33
Alignment explanation
Indices: 8737--8817 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
8727 GTTGTGCGCA
*
8737 GATGCCCCATTCGATGGCCGATTGTCGCCGGTT
1 GATGCCCCATGCGATGGCCGATTGTCGCCGGTT
* * * *
8770 GATGCCTCATGCGATGGCTGGTTGTGGCCGGTT
1 GATGCCCCATGCGATGGCCGATTGTCGCCGGTT
*
8803 -A--CTCCATGCGATGGC
1 GATGCCCCATGCGATGGC
8818 GCATGCGATG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 12 0.29
32 1 0.02
33 28 0.68
ACGTcount: A:0.12, C:0.27, G:0.33, T:0.27
Consensus pattern (33 bp):
GATGCCCCATGCGATGGCCGATTGTCGCCGGTT
Done.